Micro and nanofluidic systems are ideal platforms for breakthrough bioanalytical tools. In particular, transport in nanoscale channels has been shown to be different than microscale systems because of unique coupled physics associated with wall interactions, electrokinetic surface phenomena and hydrodynamic confinement. Furthermore, understanding the effects of reaction kinetics during capillary electrophoresis is necessary for reliable bioanalytical tools with reacting species. We present experimental data and numerical simulation to elucidate the dominant physics at these lengths scales toward enabling nanofluidic bioanalytical devices. First, we present an experimental study to measure the effect channel height and ionic strength on the electrophoretic mobility of spherical nanoparticles and short single strand (ss) and double strand (ds) DNA with channel depths ranging from 20 microns to 100 nm.

We find increased hydrodynamic drag in confinement, nanoparticle rotation effects for spherical analytes in sheer flows, non-uniform electro-osmotic velocity profiles, and electrostatic repulsion of thick electric double layers to be important effects on transport. Second, we present an experimental study of electrokinetic separations of short, complementary ss and dsDNA in microchannels. We find different phenomena are significant for the three different DNA lengths in the study (10nt, 20nt, and 50nt). Reaction kinetic effects are significant for the shortest length DNA, where the melting temperature is comparable to room temperature. For longer 20 and 50nt DNA, the melting temperatures are sufficiently high and reaction kinetic effects are constant. In addition, the 50 nt ssDNA contour length is greater than the persistence length and we find changes in electrophoretic mobility with ionic strength resulting from changes in conformation.

Finally, we present numerical simulations of the previous study on separations of reacting DNA. Reaction kinetics can affect the equilibrium ratio of ss to dsDNA which influences transport by shifting the observed electrophoretic mobility of the dsDNA peak away from the true electrophoretic mobility. We perform parametric simulations of relevant parameters and find the initial plug width, analyte concentration and kinetic rate constants are the important parameters on the observed dsDNA peak. In addition, we use our model to determine reaction kinetic parameters (ie KD) of experimental data.